def perform_ik(model_file, trc_file, results_dir):
"""Performs Inverse Kinematics using OpenSim.
Parameters
----------
model_file: str
OpenSim model (.osim)
trc_file: str
the experimentally measured marker trajectories (.trc)
results_dir: str
directory to store the results
"""
model = opensim.Model(model_file)
model.initSystem()
marker_data = opensim.MarkerData(trc_file)
name = os.path.basename(trc_file)[:-4]
ik_tool = opensim.InverseKinematicsTool()
task_set = ik_tool.getIKTaskSet()
construct_ik_task_set(model, marker_data, task_set)
ik_tool.setName(name)
ik_tool.setModel(model)
ik_tool.setStartTime(marker_data.getStartFrameTime())
ik_tool.setEndTime(marker_data.getLastFrameTime())
ik_tool.setMarkerDataFileName(trc_file)
ik_tool.setResultsDir(results_dir)
ik_file = results_dir + name + '_ik.mot'
ik_tool.setOutputMotionFileName(ik_file)
ik_tool.run()
return ik_file
def inverseKinematics():
import os
import re
import shutil
import opensim as osim
import directories
# Global Directories
allDir = list(directories.main(directories))
parentDir = allDir[0]
paramsDir = allDir[1]
subID = allDir[4]
subResultsDir = allDir[5]
ikResultsDir = allDir[6]
# Clear Inverse Kinematics Folder
if os.path.exists(ikResultsDir):
shutil.rmtree(ikResultsDir, ignore_errors=True)
if not os.path.exists(ikResultsDir):
os.mkdir(ikResultsDir)
# Input settings File
genericSettings = paramsDir + "/setupIK.xml"
# Input trc File
dataFiles = parentDir + "/data/osDemo"
ikMarkerFileName = "subject01_walk1.trc"
ikMarkerFile = dataFiles + "/" + ikMarkerFileName
shutil.copy(ikMarkerFile, ikResultsDir + "/" + ikMarkerFileName)
# Load scaled Model
aModel = osim.Model(subResultsDir + "/" + subID + ".osim")
# Import Inverse Kinematics Tool
ikTool = osim.InverseKinematicsTool(genericSettings)
# Tell IK tool to use loaded model
ikTool.setModel(aModel)
# Get scaled marker file + data
markerData = osim.MarkerData(ikMarkerFile)
# Get Initial and Final Time
initial_time = markerData.getStartFrameTime()
final_time = markerData.getLastFrameTime()
# set IK tool for this trial
ikName = re.sub('.trc', '', ikMarkerFileName)
ikTool.setName(ikName)
ikTool.setMarkerDataFileName(ikMarkerFile)
ikTool.setStartTime(initial_time)
ikTool.setEndTime(final_time)
ikTool.setOutputMotionFileName(ikResultsDir + "/" + ikName + "_ik.mot")
# Run IK
ikTool.run()
ikTool.printToXML(ikResultsDir + "/" + "setupIK.xml")
# Clear terminal
os.system('cls' if os.name == 'nt' else 'clear')
return()
def run_ik_tool(self, trial):
model = osim.Model(self.model_input)
# initialize inverse kinematic tool from setup file
ik_tool = osim.InverseKinematicsTool(self.xml_input)
ik_tool.setModel(model)
print(f'\t{trial.stem}')
# initialize inverse kinematic tool from setup file
ik_tool = osim.InverseKinematicsTool(self.xml_input)
ik_tool.setModel(model)
# set name of input (trc) file and output (mot)
if self.prefix:
filename = f"{self.prefix}_{trial.stem}"
else:
filename = trial.stem
ik_tool.setName(filename)
ik_tool.setMarkerDataFileName(f'{trial}')
ik_tool.setOutputMotionFileName(
f"{Path(self.mot_output) / filename}.mot")
ik_tool.setResultsDir(self.mot_output)
if trial.stem in self.onsets:
# set start and end times from configuration file
start = self.onsets[trial.stem][0]
end = self.onsets[trial.stem][1]
else:
# use the trc file to get the start and end times
m = osim.MarkerData(f'{trial}')
start = m.getStartFrameTime()
end = m.getLastFrameTime(
) - 1e-2 # -1e-2 because removing last frame resolves some bug
ik_tool.setStartTime(start)
ik_tool.setEndTime(end)
ik_tool.printToXML(self.xml_output)
ik_tool.run()
def perform_ik(model_file, trc_file, results_dir, settings_dir,
opensimtools_dir, opensimplugin_dir):
"""Performs Inverse Kinematics using OpenSim.
Parameters
----------
model_file: str
OpenSim model (.osim)
trc_file: str
the experimentally measured marker trajectories (.trc)
results_dir: str
directory to store the results
"""
model = opensim.Model(model_file)
# model.set_assembly_accuracy(1e-3)
#model.initSystem()
marker_data = opensim.MarkerData(trc_file)
trial = os.path.basename(trc_file)[:-4]
ik_tool = opensim.InverseKinematicsTool()
task_set = ik_tool.getIKTaskSet()
construct_ik_task_set(model, marker_data, task_set)
ik_tool.setName(trial)
ik_tool.setModel(model)
ik_tool.setStartTime(marker_data.getStartFrameTime())
ik_tool.setEndTime(marker_data.getLastFrameTime())
ik_tool.setMarkerDataFileName(trc_file)
ik_tool.setResultsDir(results_dir)
ik_file = results_dir + trial + '_IK.mot'
ik_xml = settings_dir + trial + '_Setup_IK.xml'
ik_tool.setOutputMotionFileName(ik_file)
ik_tool.printToXML(ik_xml)
##parsing the previously created setup file and change the model_file item
ik_set_file = parse(ik_xml)
ik_set_file.getElementsByTagName(
"model_file")[0].childNodes[0].nodeValue = model_file
## save the xml file
F = open(ik_xml, "w")
ik_set_file.writexml(F)
F.close()
# run the IK tool through cmd
ik_cmd = opensimtools_dir + '\ik -S ' + ik_xml
print(os.system(ik_cmd))
return ik_file
def _load_from_setup_file(self, file_path):
# type: (str) -> None
"""
Initialize properties for the IK tool from an OpenSim Inverse Kinematics setup file. Settings for
'results_directory', 'input_directory', 'report_errors' and 'ouput_motion_file' are ignored.
"""
tool = opensim.InverseKinematicsTool(file_path)
self.accuracy = float(tool.getPropertyByName("accuracy").toString())
self.constraint_weight = float(
tool.getPropertyByName("constraint_weight").toString())
self.coordinate_file = tool.getCoordinateFileName()
self.ik_task_set = tool.getIKTaskSet().clone()
self.marker_file = tool.getMarkerDataFileName()
self.model_file = tool.getPropertyByName("model_file").toString()
self.time_final = tool.getEndTime()
self.time_start = tool.getStartTime()
def access_model(params):
hlx = params[0]
hly = params[1]
hlz = params[2]
# print('Params: %f %f %f' %(hlx,hly,hlz))
# Load model for running IK on
model = osim.Model(
r'C:\Users\llim726\Documents\infant_analysis\jw\jw_Scaled_offset.osim')
# Add geometry path to ensure the geometry files are found
path = r'C:\OpenSim 4.0\Geometry'
osim.ModelVisualizer.addDirToGeometrySearchPaths(path)
# Locate the left hip joint and edit the location of the parent (pelvis) frame
jointset = model.getJointSet()
hip_l = jointset.get('hip_l')
# print('Translation before: %f %f %f' % (hip_l.get_frames(0).get_translation()[0],hip_l.get_frames(0).get_translation()[1],hip_l.get_frames(0).get_translation()[2]))
hip_l.get_frames(0).set_translation(osim.Vec3(hlx, hly, hlz))
s = model.initSystem()
#model.printToXML(r"C:\Users\llim726\Documents\infant_analysis\jw\jw_Scaled_changing.osim")
# print('Translation after: %f %f %f' % (hip_l.get_frames(0).get_translation()[0],hip_l.get_frames(0).get_translation()[1],hip_l.get_frames(0).get_translation()[2]))
# Load preconfigured IK settings file - create this using the IKTool GUI and save the necessary parameters
ik_settings = osim.InverseKinematicsTool(
r'C:\Users\llim726\Documents\infant_analysis\jw\jw_ik_tools.xml')
ik_taskset = ik_settings.getIKTaskSet()
ik_taskset.printToXML(
r"C:\Users\llim726\Documents\infant_analysis\jw\iktaskset.xml")
# Apply IK settings to the loaded model and run
ik_settings.setOutputMotionFileName(
r'C:\Users\llim726\Documents\infant_analysis\jw\opt_ik.mot')
#ik_settings.setName(r'G:\My Drive\infant_analysis\4_opensim\jw\jw_Scaled.osim')
ik_settings.setModel(model)
# ik_settings.run()
# ik_settings.printToXML(r"C:\Users\llim726\Documents\infant_analysis\jw\jw_ik_tools.xml")
# # Open log file to read in the IK RMS errors
# f = open(r'C:\Users\llim726\Documents\infant_analysis\out.log', 'r')
# ik_log = f.readlines()
# # Get the start of the Error output of the most recent IK
# for i in range(len(ik_log)):
# if ik_log[i] == 'Running tool .\n':
# rmse_start = i+1
# if not rmse_start:
# sys.exit('No error output found in out.log.')
#
# for i in range(rmse_start,len(ik_log)):
# ind_start = ik_log[i].find('RMS=')
# ind_end = ik_log[i].find(', max')
# if ind_start == -1:
# check = ik_log[i].find('completed')
# if check: # end of results found, can generate the rms array
# break
# elif i == rmse_start:
# rmse = np.array(float(ik_log[i][ind_start+4:ind_end-1]))
# else:
# rmse = np.vstack((rmse,float(ik_log[i][ind_start+4:ind_end-1])))
ik_setup_file = r"C:\Users\llim726\Documents\infant_analysis\jw\jw_ik_tools.xml"
# Create InverseKinematicsTool.
ik_tool = InverseKinematicsTool(ik_setup_file)
ik_tool.model = model
rmse = ik_tool.solve()
# Calculate the mean RMSE
mean_rmse = np.mean(rmse)
print(mean_rmse)
return mean_rmse
Initialize properties for the IK tool from an OpenSim Inverse Kinematics setup file. Settings for
'results_directory', 'input_directory', 'report_errors' and 'ouput_motion_file' are ignored.
"""
tool = opensim.InverseKinematicsTool(file_path)
self.accuracy = float(tool.getPropertyByName("accuracy").toString())
self.constraint_weight = float(
tool.getPropertyByName("constraint_weight").toString())
self.coordinate_file = tool.getCoordinateFileName()
self.ik_task_set = tool.getIKTaskSet().clone()
self.marker_file = tool.getMarkerDataFileName()
self.model_file = tool.getPropertyByName("model_file").toString()
self.time_final = tool.getEndTime()
self.time_start = tool.getStartTime()
if __name__ == "__main__":
# Set paths to model and marker data.
ik_setup_file = r"C:\Users\llim726\Documents\infant_analysis\jw\jw_ik_tools_changing.xml"
# Create InverseKinematicsTool.
ik_tool = InverseKinematicsTool(ik_setup_file)
rmse = ik_tool.solve()
ik_tool_opensim = opensim.InverseKinematicsTool(ik_setup_file)
ik_tool_opensim.run()
#assert np.isclose(rmse[-1], 0.0158721)
pass
def run_tracking_problem(self, root_dir, config):
modelProcessor = self.create_model_processor(root_dir,
for_inverse=False,
config=config)
model = modelProcessor.process()
model.initSystem()
# Count the number of Force objects in the model. We'll use this to
# normalize the control effort cost.
numForces = 0
for actu in model.getComponentsList():
if (actu.getConcreteClassName().endswith('Muscle') or
actu.getConcreteClassName().endswith('Actuator')):
numForces += 1
# Construct the base tracking problem
# -----------------------------------
track = osim.MocoTrack()
track.setName('tracking_walking')
track.setModel(modelProcessor)
if self.coordinate_tracking:
tableProcessor = osim.TableProcessor(os.path.join(root_dir,
'resources/Rajagopal2016/coordinates.mot'))
tableProcessor.append(osim.TabOpLowPassFilter(6))
tableProcessor.append(osim.TabOpUseAbsoluteStateNames())
track.setStatesReference(tableProcessor)
track.set_states_global_tracking_weight(
config.tracking_weight / (2 * model.getNumCoordinates()))
# Don't track some pelvis coordinates to avoid poor walking motion
# solutions.
stateWeights = osim.MocoWeightSet()
weightList = list()
weightList.append(('/jointset/ground_pelvis/pelvis_ty/value', 0))
weightList.append(('/jointset/ground_pelvis/pelvis_tz/value', 0))
weightList.append(('/jointset/ground_pelvis/pelvis_list/value', 0))
weightList.append(('/jointset/ground_pelvis/pelvis_tilt/value', 0))
weightList.append(('/jointset/ground_pelvis/pelvis_rotation/value', 0))
weightList.append(('/jointset/hip_r/hip_rotation_r/value', 0))
# weightList.append(('/jointset/hip_r/hip_adduction_r/value', 0))
weightList.append(('/jointset/hip_l/hip_rotation_l/value', 0))
# weightList.append(('/jointset/hip_l/hip_adduction_l/value', 0))
# weightList.append(('/jointset/ankle_r/ankle_angle_r/value', 10))
# weightList.append(('/jointset/ankle_l/ankle_angle_l/value', 10))
for weight in weightList:
stateWeights.cloneAndAppend(osim.MocoWeight(weight[0], weight[1]))
track.set_states_weight_set(stateWeights)
track.set_apply_tracked_states_to_guess(True)
# track.set_scale_state_weights_with_range(True);
else:
track.setMarkersReferenceFromTRC(os.path.join(root_dir,
'resources/Rajagopal2016/markers.trc'))
track.set_markers_global_tracking_weight(
config.tracking_weight / (2 * model.getNumMarkers()))
iktool = osim.InverseKinematicsTool(os.path.join(root_dir,
'resources/Rajagopal2016/ik_setup_walk.xml'))
iktasks = iktool.getIKTaskSet()
markerWeights = osim.MocoWeightSet()
for marker in model.getComponentsList():
if not type(marker) is osim.Marker: continue
for i in np.arange(iktasks.getSize()):
iktask = iktasks.get(int(i))
if iktask.getName() == marker.getName():
weight = osim.MocoWeight(iktask.getName(),
iktask.getWeight())
markerWeights.cloneAndAppend(weight)
track.set_markers_weight_set(markerWeights)
track.set_allow_unused_references(True)
track.set_track_reference_position_derivatives(True)
track.set_control_effort_weight(config.effort_weight / numForces)
track.set_initial_time(self.initial_time)
track.set_final_time(self.half_time)
track.set_mesh_interval(self.mesh_interval)
# Customize the base tracking problem
# -----------------------------------
study = track.initialize()
problem = study.updProblem()
problem.setTimeBounds(self.initial_time,
[self.half_time-0.2, self.half_time+0.2])
# Set the initial values for the lumbar and pelvis coordinates that
# produce "normal" walking motions.
problem.setStateInfo('/jointset/back/lumbar_extension/value', [], -0.12)
problem.setStateInfo('/jointset/back/lumbar_bending/value', [], 0)
problem.setStateInfo('/jointset/back/lumbar_rotation/value', [], 0.04)
problem.setStateInfo('/jointset/ground_pelvis/pelvis_tx/value', [], 0.446)
problem.setStateInfo('/jointset/ground_pelvis/pelvis_tilt/value', [], 0)
problem.setStateInfo('/jointset/ground_pelvis/pelvis_list/value', [], 0)
problem.setStateInfo('/jointset/ground_pelvis/pelvis_rotation/value', [], 0)
# Update the control effort goal to a cost of transport type cost.
effort = osim.MocoControlGoal().safeDownCast(
problem.updGoal('control_effort'))
effort.setDivideByDisplacement(True)
# Weight residual and reserve actuators low in the effort cost since
# they are already weak.
if config.effort_weight:
for actu in model.getComponentsList():
actuName = actu.getName()
if actu.getConcreteClassName().endswith('Actuator'):
effort.setWeightForControl(actu.getAbsolutePathString(),
0.001)
for muscle in ['psoas', 'iliacus']:
for side in ['l', 'r']:
effort.setWeightForControl(
'/forceset/%s_%s' % (muscle, side), 0.25)
speedGoal = osim.MocoAverageSpeedGoal('speed')
speedGoal.set_desired_average_speed(1.235)
problem.addGoal(speedGoal)
# MocoFrameDistanceConstraint
# ---------------------------
if self.coordinate_tracking:
distanceConstraint = osim.MocoFrameDistanceConstraint()
distanceConstraint.setName('distance_constraint')
# Step width is 0.13 * leg_length
# distance = 0.10 # TODO Should be closer to 0.11.
# Donelan JM, Kram R, Kuo AD. Mechanical and metabolic determinants
# of the preferred step width in human walking.
# Proc Biol Sci. 2001;268(1480):1985–1992.
# doi:10.1098/rspb.2001.1761
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088839/
distanceConstraint.addFramePair(
osim.MocoFrameDistanceConstraintPair(
'/bodyset/calcn_l', '/bodyset/calcn_r', 0.09, np.inf))
distanceConstraint.addFramePair(
osim.MocoFrameDistanceConstraintPair(
'/bodyset/toes_l', '/bodyset/toes_r', 0.06, np.inf))
# distanceConstraint.addFramePair(
# osim.MocoFrameDistanceConstraintPair(
# '/bodyset/calcn_l', '/bodyset/toes_r', distance, np.inf))
# distanceConstraint.addFramePair(
# osim.MocoFrameDistanceConstraintPair(
# '/bodyset/toes_l', '/bodyset/calcn_r', distance, np.inf))
distanceConstraint.setProjection("vector")
distanceConstraint.setProjectionVector(osim.Vec3(0, 0, 1))
problem.addPathConstraint(distanceConstraint)
# Symmetry constraints
# --------------------
statesRef = osim.TimeSeriesTable('tracking_walking_tracked_states.sto')
initIndex = statesRef.getNearestRowIndexForTime(self.initial_time)
symmetry = osim.MocoPeriodicityGoal('symmetry')
# Symmetric coordinate values (except for pelvis_tx) and speeds.
for coord in model.getComponentsList():
if not type(coord) is osim.Coordinate: continue
coordName = coord.getName()
coordValue = coord.getStateVariableNames().get(0)
coordSpeed = coord.getStateVariableNames().get(1)
if coordName.endswith('_r'):
symmetry.addStatePair(osim.MocoPeriodicityGoalPair(
coordValue, coordValue.replace('_r/', '_l/')))
symmetry.addStatePair(osim.MocoPeriodicityGoalPair(
coordSpeed, coordSpeed.replace('_r/', '_l/')))
elif coordName.endswith('_l'):
symmetry.addStatePair(osim.MocoPeriodicityGoalPair(
coordValue, coordValue.replace('_l/', '_r/')))
symmetry.addStatePair(osim.MocoPeriodicityGoalPair(
coordSpeed, coordSpeed.replace('_l/', '_r/')))
elif (coordName.endswith('_bending') or
coordName.endswith('_rotation') or
coordName.endswith('_tz') or
coordName.endswith('_list')):
# This does not include hip rotation,
# because that ends with _l or _r.
symmetry.addStatePair(osim.MocoPeriodicityGoalPair(
coordValue))
symmetry.addNegatedStatePair(osim.MocoPeriodicityGoalPair(
coordSpeed))
elif not coordName.endswith('_tx'):
symmetry.addStatePair(osim.MocoPeriodicityGoalPair(
coordValue))
symmetry.addStatePair(osim.MocoPeriodicityGoalPair(
coordSpeed))
symmetry.addStatePair(osim.MocoPeriodicityGoalPair(
'/jointset/ground_pelvis/pelvis_tx/speed'))
# Symmetric activations.
for actu in model.getComponentsList():
if (not actu.getConcreteClassName().endswith('Muscle') and
not actu.getConcreteClassName().endswith('Actuator')): continue
if actu.getName().endswith('_r'):
symmetry.addStatePair(osim.MocoPeriodicityGoalPair(
actu.getStateVariableNames().get(0),
actu.getStateVariableNames().get(0).replace('_r/', '_l/')))
elif actu.getName().endswith('_l'):
symmetry.addStatePair(osim.MocoPeriodicityGoalPair(
actu.getStateVariableNames().get(0),
actu.getStateVariableNames().get(0).replace('_l/', '_r/')))
elif (actu.getName().endswith('_bending') or
actu.getName().endswith('_rotation') or
actu.getName().endswith('_tz') or
actu.getName().endswith('_list')):
symmetry.addNegatedStatePair(osim.MocoPeriodicityGoalPair(
actu.getStateVariableNames().get(0),
actu.getStateVariableNames().get(0)))
else:
symmetry.addStatePair(osim.MocoPeriodicityGoalPair(
actu.getStateVariableNames().get(0),
actu.getStateVariableNames().get(0)))
problem.addGoal(symmetry)
# Contact tracking
# ----------------
forceNamesRightFoot = ['forceset/contactSphereHeel_r',
'forceset/contactLateralRearfoot_r',
'forceset/contactLateralMidfoot_r',
'forceset/contactLateralToe_r',
'forceset/contactMedialToe_r',
'forceset/contactMedialMidfoot_r']
forceNamesLeftFoot = ['forceset/contactSphereHeel_l',
'forceset/contactLateralRearfoot_l',
'forceset/contactLateralMidfoot_l',
'forceset/contactLateralToe_l',
'forceset/contactMedialToe_l',
'forceset/contactMedialMidfoot_l']
if self.contact_tracking:
contactTracking = osim.MocoContactTrackingGoal('contact', 0.001)
contactTracking.setExternalLoadsFile(
'resources/Rajagopal2016/grf_walk.xml')
contactTracking.addContactGroup(forceNamesRightFoot, 'Right_GRF')
contactTracking.addContactGroup(forceNamesLeftFoot, 'Left_GRF')
contactTracking.setProjection("plane")
contactTracking.setProjectionVector(osim.Vec3(0, 0, 1))
problem.addGoal(contactTracking)
# Configure the solver
# --------------------
solver = osim.MocoCasADiSolver.safeDownCast(study.updSolver())
solver.resetProblem(problem)
solver.set_optim_constraint_tolerance(1e-3)
solver.set_optim_convergence_tolerance(1e-3)
solver.set_multibody_dynamics_mode('implicit')
solver.set_minimize_implicit_multibody_accelerations(True)
solver.set_implicit_multibody_accelerations_weight(
1e-6 / model.getNumCoordinates())
solver.set_implicit_multibody_acceleration_bounds(
osim.MocoBounds(-200, 200))
# Set the guess
# -------------
# Create a guess compatible with this problem.
guess = solver.createGuess()
# Load the inverse problem solution and set its states and controls
# trajectories to the guess.
inverseSolution = osim.MocoTrajectory(
os.path.join(root_dir, self.inverse_solution_relpath))
inverseStatesTable = inverseSolution.exportToStatesTable()
guess.insertStatesTrajectory(inverseStatesTable, True)
# Changing this initial guess has a large negative effect on the
# solution! Lots of knee flexion.
# guess.setState('/jointset/ground_pelvis/pelvis_ty/value',
# osim.Vector(guess.getNumTimes(), 1.01))
inverseControlsTable = inverseSolution.exportToControlsTable()
guess.insertControlsTrajectory(inverseControlsTable, True)
solver.setGuess(guess)
# Solve and print solution.
# -------------------------
solution = study.solve()
solution.write(self.get_solution_path(root_dir, config))
# Create a full gait cycle trajectory from the periodic solution.
fullTraj = osim.createPeriodicTrajectory(solution)
fullTraj.write(self.get_solution_path_fullcycle(root_dir, config))
# Compute ground reaction forces generated by contact sphere from the
# full gait cycle trajectory.
externalLoads = osim.createExternalLoadsTableForGait(
model, fullTraj, forceNamesRightFoot, forceNamesLeftFoot)
osim.writeTableToFile(externalLoads,
self.get_solution_path_grfs(root_dir, config))
# #Run the torque driven marker tracking problem
# torqueDrivenMarkerTracking(startTime = startTime,endTime = endTime,meshInterval = 0.05,
# scaledModelFile = 'scaledModelAdjusted.osim',
# grfXml = 'Jog05_grf.xml', trcFile = 'Jog05_virtualMarkers.trc',
# ikTasksXml = 'ikTasks.xml')
##### Marker tracking looks fairly good - compare to IK?
##### Still getting visualiser error though - weird considering it works for Moco examples?
# %% Inverse kinematics
##### TODO: could set this in osimHelper function
#Initialise IK tool
ikTool = osim.InverseKinematicsTool()
#Set model
ikTool.setModel(scaledModel)
#Set task set
ikTool.set_IKTaskSet(osim.IKTaskSet('ikTasks.xml'))
#Set marker file
ikTool.set_marker_file('Jog05_virtualMarkers.trc')
#Set times
ikTool.setStartTime(startTime)
ikTool.setEndTime(endTime)
#Set output filename
TRC_file = TRC_files[0]
path, filename = os.path.split(TRC_file)
filename, ext = os.path.splitext(filename)
MOT_file = 'MOT\\' + filename + '.mot' # Path to the output .MOT file that will be created and contain the IK results
XML_IK_file = 'XML\\' + filename + '_IK.xml' # Path to the IK XML file that will be created
# Marker Data
markerData = osim.MarkerData(TRC_file)
initial_time = markerData.getStartFrameTime()
final_time = markerData.getLastFrameTime()
# Set the IK tool
ikTool = osim.InverseKinematicsTool(XML_generic_IK_path)
ikTool.setModel(osimModel)
ikTool.setName(filename + ext)
ikTool.setMarkerDataFileName(TRC_file)
ikTool.setStartTime(initial_time)
ikTool.setEndTime(final_time)
ikTool.setOutputMotionFileName(MOT_file)
# Set the ikTool with the MarkerTask
for j in range(0, markerList.shape[0]):
ikMarkerTask = osim.IKMarkerTask()
ikMarkerTask.setName(markerList[j])
ikMarkerTask.setApply(1)
ikMarkerTask.setWeight(markerWeight[j])
ikTool.getIKTaskSet().adoptAndAppend(ikMarkerTask)
def setup_IK_xml(trial: str, model: str, directory: str, time_range: list, marker_names: list):
'''
Rewrites the IK setup xml file for a new trial
Inputs: trial: trial name, e.g., "_12Mar_ss_12ms_01"
model: model name, e.g., "AB08"
directory: output directory name
time_range: start and end times
marker_names: list of the markers names which we are using
'''
# Create an instance of the inverse kinematics tool
IK_tool = osim.InverseKinematicsTool()
# Set the name of the tool
IK_tool.setName(model)
# Set the input and results directory
IK_tool.setInputsDir(directory + "\\" + model + "\\" + trial)
IK_tool.setResultsDir(directory + "\\" + model + "\\" + trial)
# Set the time range, NOTE: Must be a double (np.float64)
IK_tool.setStartTime(np.float64(time_range[0]))
IK_tool.setEndTime(np.float64(time_range[-1]))
# Set the marker file
marker_file_name = directory + "\\" + model + "\\" + trial + "\\" + trial + ".trc"
IK_tool.setMarkerDataFileName(marker_file_name)
# Set the coordinate file
coordinate_file_name = ''
IK_tool.setCoordinateFileName(coordinate_file_name)
# Set the output motion file
output_file_name = directory + "\\" + model + "\\" + trial + "\\" + trial + "IKResults.mot"
IK_tool.setOutputMotionFileName(output_file_name)
''' Add markers and set weighting '''
# List of bony anatomical landmarkers to give high weighting
bony_landmarks = ['LMMAL','RMMAL','LLMAL','RLMAL','LASI','RASI','LPSI','RPSI']
# Create IKTaskSet
IK_task_set = IK_tool.getIKTaskSet()
# Assign markers and weights
for marker in marker_names:
IK_marker_task = osim.IKMarkerTask()
IK_marker_task.setName(marker)
if marker in bony_landmarks:
IK_marker_task.setApply(True)
IK_marker_task.setWeight(10)
else:
IK_marker_task.setApply(True)
IK_marker_task.setWeight(1)
IK_task_set.cloneAndAppend(IK_marker_task)
''' Write changes to an XML setup file '''
xml_setup_path = directory + "\\" + model + "\\" + trial + "\\" + trial + "IKSetup.xml"
IK_tool.printToXML(xml_setup_path)
''' Temporary fix for setting model name using XML parsing '''
dom = minidom.parse(xml_setup_path)
dom.getElementsByTagName("model_file")[0].firstChild.nodeValue = directory + "\\" + model + "\\" + model + ".osim"
with open(xml_setup_path, 'w') as xml_file:
dom.writexml(xml_file, addindent='\t', newl='\n', encoding='UTF-8')
scale_tool.getGenericModelMaker().processModel()
scale_tool.getModelScaler().setMarkerFileName(marker_file)
# scale_tool.getModelScaler().setOutputModelFileName(os.path.join(data_folder,scaled_model_filename))
scale_tool.getModelScaler().processModel(model, '', subject_mass)
scale_tool.getMarkerPlacer().setMarkerFileName(marker_file)
scale_tool.getMarkerPlacer().processModel(model)
scale_tool.run()
#Save Model
model.printToXML(os.path.join(location_motion_data, scaled_model_filename))
#Perform IK
ik_tool = opensim.InverseKinematicsTool(os.path.join(location_XMLs, ik_file))
ik_tool.setModel(model)
ik_tool.setName(marker_data_filenames)
ik_tool.setMarkerDataFileName(
os.path.join(location_motion_data, marker_data_filenames))
ik_tool.setStartTime(ik_start_time)
ik_tool.setEndTime(ik_end_time)
ik_tool.setOutputMotionFileName(
os.path.join(location_motion_data, save_ik_name))
ik_tool.run()
#Build external loads file and save to disk - this will be loaded in for IK and SO
external_loads = opensim.ExternalLoads(
os.path.join(location_XMLs, external_loads_xml), True)
external_loads.setLowpassCutoffFrequencyForLoadKinematics(
kinematic_filter_frequency)